GetContacts

Computing contact fingerprints from a set of static structures

The following steps will generate a contact fingerprint for a set of static structures (e.g. PDB-files solved with X-ray crystallography).

• The first step extracts atomic-level interactions from the structures.
• The second step computes residue-level frequencies (will be either 0 or 1) and renames residues according to a residue-label file that conveniently formats labels and acts as alignment.
• The third step combines the frequency files into a fingerprint heatmap.

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Example

Given two PDB-files of different molecules,

• structure_1.pdb
• structure_2.pdb

For each structure, first generate a contact list and then the set of residue contact frequencies:

  get_static_contacts.py --structure structure_1.pdb --itypes hb --output contacts_1.tsv
  get_static_contacts.py --structure structure_2.pdb --itypes hb --output contacts_2.tsv

  get_contact_frequencies.py --input_files contacts_1.tsv --itypes all --output_file resfrequencies_1.tsv
  get_contact_frequencies.py --input_files contacts_2.tsv --itypes all --output_file resfrequencies_2.tsv
        

Next, the residue contact frequencies are combined a plot is written to a png file:

  get_contact_fingerprints.py --input_frequencies resfrequencies_1.tsv resfrequencies_2.tsv \
                              --column_headers "Structure 1" "Structure 2" \
                              --plot_output fingerprint.png
        

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